Abstract

High-throughput data is increasingly being integrated into the fields of biology, molecular biology, and pharmacology. However, a difficult problem has been the rapid and fluid access to and integration of the data, which tends to reside in huge unwieldy databases. One set of cell lines with substantial potential for benefit from this type of access and integration is the NCI-60 cancerous cell lines. We present here a set of tools within our CellMiner web-application designed to address this need for the areas of transcript expression, microRNA expression, gene DNA copy number, variant status, and drug activity. CellMiner allows the user to rapidly access data for relative levels of transcript expression for 26,065 genes, 360 microRNAs, and 20,602 compounds including 102 Food and Drug Administration (FDA)-approved drugs. These levels in turn create patterns across the NCI-60 that can be compared to one another using our “pattern match” tool. Together, these tools allow one to query the data for potential relationships between these parameters, in a manner specific to a users area of expertise and interest, in a rapid and flexible manner without the need for expertise in computer science or bioinformatics. Comparisons of transcript/drug will be demonstrated with SLFN11/topotecan; variant/drug with BRAF V600E/vemurafinib; colon tissue-of origin specific genes with TRIM15, RNF43, and VIL1; and DNA copy number change with CDKN2A (p16). The data are publicly available at http://discover.nci.nih.gov/cellminer.